Snakemake Report

Jobs 2

Input files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_{variants}/{method}/.completed

Output files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_{variants}/{method}/.pipeline

Code

1	`touch {output}`

Jobs 2

Input files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_{variants}/{method}/temp/.tmp

Output files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_{variants}/{method}/.completed

Code

1	`touch {output}`

Jobs 2

Input files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_{variants}/vireo/nclones20/enrichment/volcano_Fisher_foldNorm.png
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_{variants}/vireo/nclones40/enrichment/volcano_Fisher_foldNorm.png
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_{variants}/vireo/nclones100/enrichment/volcano_Fisher_foldNorm.png

Output files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_{variants}/vireo/temp/.tmp

Code

1	`touch {output}`

Jobs 6

Input files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_{variants}/vireo/nclones{nclones}/cells_meta.tsv

Output files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_{variants}/vireo/nclones{nclones}/enrichment/volcano_Fisher_foldNorm.png

Code

1	`python {params.script} {params.clones_indir} {params.OUTDIR} {params.nclones} {params.samples}`

Jobs 3

Input files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/multiplex/multiplex.ipynb

Output files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_simple/vireo/nclones{nclones}/donor0.labels.png
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_simple/vireo/nclones{nclones}/donor1.labels.png
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_simple/vireo/nclones{nclones}/donor2.labels.png
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_simple/vireo/nclones{nclones}/donor3.labels.png
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_simple/vireo/nclones{nclones}/donor0.variants.labels.png
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_simple/vireo/nclones{nclones}/donor1.variants.labels.png
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_simple/vireo/nclones{nclones}/donor2.variants.labels.png
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_simple/vireo/nclones{nclones}/donor3.variants.labels.png
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_simple/vireo/nclones{nclones}/cells_meta.tsv

Code

1	`papermill -p INDIR {params.INDIR} -p OUTDIR {params.OUTDIR} -p N_DONORS {params.N_DONORS} -p nclones {params.nclones} {params.notebook} {params.OUTDIR}/output.ipynb`

Jobs 1

Input files

{outdir}/cellSNP.tag.AD.mtx

Output files

{outdir}/multiplex/multiplex.ipynb
{outdir}/multiplex/multiplex_AF_SNPs_all_afFilt.png
{outdir}/multiplex/multiplex_clusters_all.labels.png

Code

papermill -p INDIR {params.INDIR} -p OUTDIR {params.OUTDIR} -p N_DONORS {params.N_DONORS} -p sample_names {params.sample_names} -p to_elbo {params.to_elbo} --log-output {params.notebook} {output.note}

Jobs 1

Input files

at 0x7fb1e659d950>

Output files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/cellSNP.tag.AD.mtx

Code

1	`python -m src.pseudo_batch {params.outdir} {params.indirs} --num_cells {params.num_cells} --is_prop {params.is_prop} --samples {params.prefix}`

Jobs 2

Input files

{output}/data/{sample}/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/{sample}.variant.rds

Output files

{output}/data/{sample}/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/{sample}/vireoIn/cellSNP.tag.AD.mtx

Code

1	`python src/mgatk_to_vireo.py {params.indir} {params.outdir} {params.sample}`

Jobs 2

Input files

{outdir}/{sample}.coverage.txt
{outdir}/chrM_refAllele.txt

Output files

{outdir}/mgatk/{sample}.variant.rds
{outdir}/mgatk/{sample}.variantQC.png

Code

1	`./R_scripts/wrap_mgatk.R {params.data_dir} mgatk/{params.sample} FALSE`

Jobs 2

Input files

{output}/data/{sample}/MT/cellr_{cellrbc}/numread_{num_read}/{sample}.coverage.strands.txt.gz

Output files

{output}/data/{sample}/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/{sample}.coverage.txt
{output}/data/{sample}/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/af_by_cell.tsv

Code

1	`python src/mtpreproc/calculate_AF_by_cell.py {params.concat_d} {output.af} {params.ref_fa} {params.name} {params.filt_params}`

Rule properties
Input files
Jobs	2
{output}/data/{sample}/MT/scPileup_concat_{num_read}/numread_{num_read}_all.coverage.strands.txt.gz {output}/data/{sample}/MT/cellr_{cellrbc}/{sample}_barcode_data.p
Output files
{output}/data/{sample}/MT/cellr_{cellrbc}/numread_{num_read}/{sample}.coverage.strands.txt.gz

Jobs 2

Input files

{output}/data/{sample}/MT/scPileup_concat_{num_read}/numread_{num_read}_all.coverage.minus.txt

Output files

{output}/data/{sample}/MT/scPileup_concat_{num_read}/numread_{num_read}_all.coverage.strands.txt.gz

Code

1	`python src/mtpreproc/scPileup_mergeStrands.py {params.concat_dir} {params.samplename} > {log}`

Jobs 2

Input files

{output}/data/{sample}/MT/{sample}_barcode_data.p

Output files

{output}/data/{sample}/MT/cellr_{cellrbc}/{sample}_barcode_data.p

Code

1	`python src/mtpreproc/filter_barcodes.py {input} {params} {output}`

Jobs 2

Input files

{output}/data/{sample}/MT/{sample}.MT.bam
{output}/data/{sample}/MT/{sample}.MT.bam.bai

Output files

{output}/data/{sample}/MT/{sample}_barcode_data.p

Code

1	`python src/mtpreproc/bam_barcodes_function.py {input.mt_bam} {output} {params.mt_chr}`

Rule properties
Input files
Jobs	2
{output}/data/{sample}/00_bam/{sample}.bam.bai
Output files
{output}/data/{sample}/MT/{sample}.MT.bam {output}/data/{sample}/MT/{sample}.MT.bam.bai

Jobs 2

Input files

{output}/data/{sample}/00_bam/{sample}.bam

Output files

{output}/data/{sample}/00_bam/{sample}.bam.bai

Code

1	`samtools index {input}`

Jobs 2

Input files

Output files

{output}/data/{sample}/00_bam/{sample}.bam

Code

1	`ln -sr {input} {output}`

Jobs 6

Output files

{outdir}/chrM_refAllele.txt

Code

1	`cp {params} {output}`

Rule properties
Input files
Jobs	3
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_mgatkdonor/vireo/nclones{nclones}/donor0_cells_meta.tsv {output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_mgatkdonor/vireo/nclones{nclones}/donor1_cells_meta.tsv {output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_mgatkdonor/vireo/nclones{nclones}/donor2_cells_meta.tsv {output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_mgatkdonor/vireo/nclones{nclones}/donor3_cells_meta.tsv
Output files
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_mgatkdonor/vireo/nclones{nclones}/cells_meta.tsv

Jobs 12

Input files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_mgatkdonor/vireo/donor{d}/mgatk_donor/cellSNP.tag.AD.mtx
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_mgatkdonor/vireo/donor{d}/mgatk_donor/cells_meta.tsv

Output files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_mgatkdonor/vireo/nclones{nclones}/donor{d}.labels.png
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_mgatkdonor/vireo/nclones{nclones}/donor{d}.variants.labels.png
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_mgatkdonor/vireo/nclones{nclones}/donor{d}_cells_meta.tsv

Code

1	`papermill -p INDIR {params.INDIR} -p OUTDIR {params.OUTDIR} -p donor {params.d} -p nclones {params.nclones} {params.notebook} {params.OUTDIR}/output.ipynb`

Jobs 4

Input files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_mgatkdonor/donor{d}/mgatk_donor/d{d}.variant.rds

Output files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_mgatkdonor/vireo/donor{d}/mgatk_donor/cellSNP.tag.AD.mtx

Code

1	`python src/mgatk_to_vireo.py {params.indir} {params.outdir} {params.donor}`

Jobs 4

Input files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_mgatkdonor/donor{d}/d{d}.coverage.txt
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_mgatkdonor/donor{d}/chrM_refAllele.txt

Output files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_mgatkdonor/donor{d}/mgatk_donor/d{d}.variant.rds

Code

1	`./R_scripts/wrap_mgatk.R {params.data_dir} mgatk_donor/{params.donor} FALSE`

Jobs 1

Input files

{output}/data/Control/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/Control.coverage.txt
{output}/data/Flt3l/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/Flt3l.coverage.txt
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/multiplex/multiplex.ipynb

Output files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_mgatkdonor/donor0/d0.coverage.txt
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_mgatkdonor/donor1/d1.coverage.txt
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_mgatkdonor/donor2/d2.coverage.txt
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_mgatkdonor/donor3/d3.coverage.txt

Code

""" Snakemake Script. Don't import snakemake."""

import pandas as pd
from os.path import dirname, join
import click

print('input', snakemake.input)
print('output ', snakemake.output)
#for sample, infile in zip(snakemake.params.samples, snakemake.input):
cells_meta = pd.read_csv(snakemake.params.cells_meta , sep='\t')
sample = snakemake.params.sample

for d, df in cells_meta.groupby('donor'):
    d = int(d)
    nt_pileups = {}
    cond_positions = {}
    nt_pileups["coverage"] = pd.DataFrame()

    for ind, curr_cov_f in enumerate(snakemake.input.cov):
        print('curr_cov_f ', curr_cov_f)
        curr_samp_cov = pd.read_csv(curr_cov_f,
                                    header=None)  # load sample coverage
        condition = sample[ind]
        curr_samp_donor_df = df[
            df["condition"] == condition]  # Condition-donors
        filt_df = curr_samp_cov.loc[
            curr_samp_cov[1].isin(curr_samp_donor_df["raw ID"])]
        # print('filt_df', filt_df.head())
        filt_df[1] = filt_df[1] + "_" + sample[ind]
        cond_positions[sample[ind]] = set(filt_df[0].values)
        nt_pileups["coverage"] = nt_pileups["coverage"].append(filt_df,
                                                               ignore_index=True)

    # Filter by overlapping positions:
    pos_to_keep = list(cond_positions.values())[0].intersection(
        *list(cond_positions.values()))
    nt_pileups["coverage"] = nt_pileups["coverage"][
        nt_pileups["coverage"][0].isin(pos_to_keep)]

    # Some cells may not be present anymore, need to store them.
    cells_to_keep = set(nt_pileups["coverage"][1])

    # Save coverage and depth
    nt_pileups["coverage"].to_csv(str(snakemake.output[int(d)]), index=False,
                                  header=False)
    depth = nt_pileups["coverage"].groupby(1).sum()[2] / 16569
    depth.to_csv(join(dirname(snakemake.output[int(d)]), f"d{d}.depthTable.txt"),
                 sep='\t', header=False)

    # Filter for the nucleotides as well
    for nuc in ["C", "A", "G", "T"]:
        nt_pileups[nuc] = pd.DataFrame()
        for ind, curr_cov_f in enumerate(snakemake.input.cov):
            curr_samp_cov = pd.read_csv(join(dirname(curr_cov_f),
                                             f"{sample[ind]}.{nuc}.txt"),
                                        header=None)  # load sample coverage
            condition = sample[ind]
            curr_samp_donor_df = df[df["condition"] == condition]
            filt_df = curr_samp_cov.loc[curr_samp_cov[1].isin(
                curr_samp_donor_df["raw ID"])]  # Filter by donor
            ## Filter by positions to keep and cells
            filt_df[1] = filt_df[1] + "_" + sample[ind]
            filt_df = filt_df[((filt_df[0].isin(pos_to_keep)) & (
                filt_df[1].isin(cells_to_keep)))]

            nt_pileups[nuc] = nt_pileups[nuc].append(filt_df,
                                                     ignore_index=True)
        # Save coverage
        nt_pileups[nuc].to_csv(
            join(dirname(snakemake.output[int(d)]), f"d{d}.{nuc}.txt"),
            header=False, index=False)

    cells_meta = cells_meta[cells_meta["ID"].isin(cells_to_keep)]
    cells_meta.to_csv(join(dirname(snakemake.output[int(d)]), "cells_meta.tsv"),
                      sep='\t', index=False)

Jobs 4

Input files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/multiplex/multiplex.ipynb

Output files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/clones/variants_mgatkdonor/vireo/donor{d}/mgatk_donor/cells_meta.tsv

Code

1	`cp {params.cells_meta} {output}`

Jobs 2

Input files

{output}/data/{sample}/MT/cellr_{cellrbc}/numread_{num_read}/sc_coverage.csv

Output files

{output}/figures/{sample}/MT/cellr_{cellrbc}/numread_{num_read}_MT_position_coverage.png
{output}/figures/{sample}/MT/cellr_{cellrbc}/numread_{num_read}_MT_position.png

Code

1	`python src/figures/plot_heatmap_coverage.py plot {input.sc_coverage_f} {output.save_f_heat} {output.save_f_coverage}`

Jobs 2

Input files

{output}/data/{sample}/MT/scPileup_concat_{num_read}/numread_{num_read}_all.coverage.strands.txt.gz
{output}/data/{sample}/MT/cellr_{cellrbc}/{sample}_barcode_data.p

Output files

{output}/data/{sample}/MT/cellr_{cellrbc}/numread_{num_read}/sc_coverage.csv

Code

1	`python src/figures/plot_heatmap_coverage.py sc_mt {input.barcode_p} {input.all} {output.sc_coverage_f} {params.maxBP}`

Jobs 1

Input files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/multiplex/multiplex.ipynb

Output files

{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/multiplex/dendrograms/figures/donor0_dendrogram.png
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/multiplex/dendrograms/figures/donor1_dendrogram.png
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/multiplex/dendrograms/figures/donor2_dendrogram.png
{output}/data/merged/MT/cellr_{cellrbc}/numread_{num_read}/filters/minC{mincells}_minR{minreads}_topN{topN}_hetT{hetthresh}_hetC{minhetcells}_hetCount{hetcountthresh}_bq{bqthresh}/mgatk/vireoIn/multiplex/dendrograms/figures/donor3_dendrogram.png

Code

1	`papermill -p INDIR {params.INDIR} -p OUTDIR {params.OUTDIR} -p sample_names {params.sample_names} -p N_DONORS {params.N_DONORS} {params.notebook} {params.note}`

Workflow

Other

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